Fig. 3

Phylogeny of 262 clinical Haemophilus spp. isolates from a German cohort. The phylogenetic tree is based on the alignment of 104 core genes (present in at least 90% of the strains). A Kraken2 read classification output. The length of a bar is proportional to the percentage of reads that are assigned to the respective taxon (as indicated by the color). One H. influenzae culture (located in the phylogenetic tree in the “fuzzy” clade) was likely contaminated with a Streptococcus sp. strain (19% of the reads assigned to this species) and another one with an Aggregatibacter sp. strain (52% reads assigned to this species). B Presence/absence of marker genes included in our new taxonomic classification database. C Final classification output of the decision algorithm. Mixed colors represent the presence of multiple full marker patterns, indicating multiple distinct Haemophilus species. D Presence/absence of antibiotic resistance genes included in a public resistance database. Color codes correlate to the antibiotic class to which the gene confers resistance: aminoglycosides (Agly), β-lactam antibiotics (Bla), phenicols (Phe), trimethoprim (Tmt), macrolide-lincosamide-streptogramin (MLS), sulfonamides (Sul), and tetracyclines (Tet)